#-------------------------------------------------------------------------------
# Stage 2.4: NPT integration for 200 ps with a timestep of 1 fs
# Temperature 298.15 K
# Pressure 1 atm
#-------------------------------------------------------------------------------
# Fix shake is needed for water in pcff+
fix shaken all shake .0001 20 50000 a 2 b 2
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
8303 = # of frozen angles
find clusters CPU = 0.002 seconds
reset_timestep 0
thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke
thermo ${Nthermo}
thermo 0
fix 1 movable npt temp 298.15 298.15 100 iso 1 1 100 drag 0 mtk yes nreset 4000
fix 2 movable ave/time 1 19999 20000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_averages.txt off 1
fix 3 movable ave/time 20 1 20 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.4_instantaneous.txt
restart 200000 2.4.restart
dump sci all custom 20000 2.4.xyz id mol type q xs ys zs
timestep 1
run 200000
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:340)
G vector (1/distance) = 0.32104129
grid = 72 72 60
stencil order = 5
estimated absolute RMS force accuracy = 0.0035806992
estimated relative force accuracy = 1.0783169e-05
using double precision KISS FFT
3d grid and FFT values/proc = 23125 10368
generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule
SHAKE stats (type/ave/delta/count) on step 0
2 0.998003 0.808999 24909
2 95.7868 77.76 8303
Per MPI rank memory allocation (min/avg/max) = 14.39 | 14.82 | 15.37 Mbytes
Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng
0 1e-06 18657.891 400035.3 0.91038687 428.46899 109.25468 1019.0606 0 0 86843.462 283410.92 -936.592 -792155.49 -420772.79 24261.4
SHAKE stats (type/ave/delta/count) on step 50000
2 0.970014 1.45634e-06 24909
2 103.7 0.000108471 8303
SHAKE stats (type/ave/delta/count) on step 100000
2 0.970007 1.65181e-06 24909
2 103.7 0.000120689 8303
SHAKE stats (type/ave/delta/count) on step 150000
2 0.970021 1.38739e-06 24909
2 103.7 0.000100157 8303
SHAKE stats (type/ave/delta/count) on step 200000
2 0.969974 1.22694e-06 24909
2 103.7 0.000100622 8303
200000 200000 227.91731 292119.83 1.2467037 302.43839 137.36188 299.40782 0 0 64050.588 257663.51 -1282.5896 -805388.91 -483238.04 17125.11
Loop time of 3529.86 on 32 procs for 200000 steps with 27300 atoms
Performance: 4.895 ns/day, 4.903 hours/ns, 56.659 timesteps/s
98.3% CPU use with 32 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1175.5 | 1260.5 | 1406.9 | 164.8 | 35.71
Bond | 0.4603 | 1.1899 | 1.9491 | 32.2 | 0.03
Kspace | 1341.5 | 1488.2 | 1574.1 | 151.2 | 42.16
Neigh | 86.428 | 86.608 | 86.864 | 1.1 | 2.45
Comm | 166.98 | 170.45 | 172.56 | 11.5 | 4.83
Output | 0.022165 | 0.027208 | 0.032041 | 1.8 | 0.00
Modify | 327.49 | 478 | 504.24 | 233.5 | 13.54
Other | | 44.81 | | | 1.27
Nlocal: 853.125 ave 899 max 813 min
Histogram: 1 2 3 7 6 5 3 1 3 1
Nghost: 7240.78 ave 7345 max 7122 min
Histogram: 1 2 2 6 4 3 3 9 1 1
Neighs: 253625 ave 277601 max 240360 min
Histogram: 4 5 5 5 4 5 1 2 0 1
Total # of neighbors = 8116011
Ave neighs/atom = 297.28978
Ave special neighs/atom = 1.892967
Neighbor list builds = 11136
Dangerous builds = 1
undump sci
restart 0
dump sci all custom 200000 2.4.xyz id mol type q xs ys zs
run 0
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:340)
G vector (1/distance) = 0.32301495
grid = 64 64 60
stencil order = 5
estimated absolute RMS force accuracy = 0.0037362879
estimated relative force accuracy = 1.125172e-05
using double precision KISS FFT
3d grid and FFT values/proc = 19573 8192
generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule
SHAKE stats (type/ave/delta/count) on step 200000
2 0.969974 1.22694e-06 24909
2 103.7 0.000100622 8303
Per MPI rank memory allocation (min/avg/max) = 14.47 | 14.73 | 15.05 Mbytes
Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng
200000 200000 74.87011 292119.83 1.2467037 302.43839 137.36188 299.40782 0 0 64050.588 262514.16 -1282.5896 -810239.62 -483238.1 17125.11
Loop time of 7.92997e-06 on 32 procs for 0 steps with 27300 atoms
118.6% CPU use with 32 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Kspace | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 7.93e-06 | | |100.00
Nlocal: 853.125 ave 899 max 813 min
Histogram: 1 2 3 7 6 5 3 1 3 1
Nghost: 7240.78 ave 7345 max 7122 min
Histogram: 1 2 2 6 4 3 3 9 1 1
Neighs: 253625 ave 277601 max 240360 min
Histogram: 4 5 5 5 4 5 1 2 0 1
Total # of neighbors = 8116011
Ave neighs/atom = 297.28978
Ave special neighs/atom = 1.892967
Neighbor list builds = 0
Dangerous builds = 0
undump sci
unfix 1
unfix 2
unfix 3
unfix shaken
log 2.5_NVT.out